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SMARTSViewer

StreamableVernalis custom KNIME nodes package version 1.28.0.v202012181313 by Vernalis (R&D), UK

Provides a SMARTSviewer visualisation of a column of SMARTs strings using the service provided by the University of Hamburg. The node performs no validation of the SMARTs strings prior to sending to the webservice. For more detailed information about the implementation see either the Help file at http://smartsview.zbh.uni-hamburg.de/smartsview/view or the following reference:
K. Schomburg, H.-C. Ehrlich, K. Stierand, M.Rarey; From Structure Diagrams to Visual Chemical Patterns, J. Chem. Inf. Model., 2010, 50, pp 1529-1535

The Communication Error Settings tab allows setting of behaviour relating to server communication problem handling. The values set are applied to each row in turn. The server will only be contacted until a successful result is returned. The settings allow the user to control the behaviour of the node should the SMARTSviewer server be functioning incorrectly. Note that it is not currently possible to cancel execution during a row, so use long delay settings with care!

Note that SMARTs strings are transferred to the remote server unencrypted, and the the server maintains an anonymous record of query SMARTs strings to aid future development.

This node was developed by Vernalis (Cambridge, UK). For feedback and more information, please contact knime@vernalis.com

Options

Select a column containing the SMARTs Strings
Select a column containing SMARTs strings for visualsation. No SMARTS validation is carried out prior to sending to the remote server, which will return a blank image for invalid SMARTS strings
Select legend type
Choose the desired legend type: Dynamic - detailed text description of each atom and bond; Static - short description of how each symbol is depicted in the visualisation
Select Visualisation modus
Element symbols uses text representation of the element symbols in the depiction

Communication Error Settings

Number of retries to contact server
Set the number of times the server will be re-contacted following a failure.
Delay between attempts (secs)
The delay period between each re-try
Ignore server errors
If set, the node will return a 'missing value' cell for each row which failed to contact the server after the defined number of attempts - allowing workflow execution to continue, otherwise node execution will fail. Setting a long delay interval (max 10 minutes) and large number of attempts (max 20) allows the workflow a chance to restore functionality (it will take over 3 hours between the first and last attempt for each row in these circumstances)
Restore Defaults
Restore the default server settings.

Input Ports

Icon
Input port containing a column of SMARTS strings, either as String, SMARTS or Smiles format

Output Ports

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The input table with the SMARTSViewer representations appended as a PNG column

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Vernalis KNIME Nodes from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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